My dog was eating Natural Choice, which is made by Nutro, which is a company involved in the food recall. I think it would give me a lot of piece of mind to switch her food, even though she eats dry food, which I know was not affected, just because of the whole prinicpal that if the manufacturers are that lax about it, it would happen again . . .

Anyway, she is almost out of food and I know usually you would do a gradual switch over . . . so now how do I make a switch over without really messing up her stomach for a while?

I would just make the switch. It's better to deal with the dog having the runs than serious health issues. You can supplement the dog's food with some plain canned pumpkin which helps balance their system.